GapMind for catabolism of small carbon sources

 

Aligments for a candidate for rocA in Phaeobacter inhibens BS107

Align Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial; P5C dehydrogenase; Aldehyde dehydrogenase family 4 member A1; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized)
to candidate GFF3619 PGA1_262p00230 betaine aldehyde dehydrogenase BetB

Query= SwissProt::Q8CHT0
         (562 letters)



>lcl|FitnessBrowser__Phaeo:GFF3619 PGA1_262p00230 betaine aldehyde
           dehydrogenase BetB
          Length = 494

 Score =  150 bits (379), Expect = 1e-40
 Identities = 134/449 (29%), Positives = 212/449 (47%), Gaps = 32/449 (7%)

Query: 93  FCYADKALLNRAIDAALAARKEWDLKPMADRAQVFLKAADMLSGPRRAEVLAKT-MVGQG 151
           F   D A ++ A+ +A+A  + W   P A R  +  +AA ++     AE LA    V  G
Sbjct: 52  FAAGDAADVDHAVTSAVAGFEIWSATPPARRCAILNEAARLMR--HEAEHLAVVECVDSG 109

Query: 152 KTVIQAEIDAA--AELIDFFRFNAKFAVELEGEQPISVPPSTNHTVYRGLEGFVAAISPF 209
           KT+ +A  D A  A L++++   A  A +L+G   +++         R   G  A I P+
Sbjct: 110 KTLAEARGDIAGSARLLEYY---AGAADKLDGRS-VNLGNDNAAFTLREPVGVTAHIVPW 165

Query: 210 NFTAIGGNLAGAPALM-GNVVLWKPSDTAMLASYAVYRILREAGLPPNIIQFVPADGPTF 268
           N+ +       APAL  G   + KP++T    +  +  +L  AGLP  ++  V   G   
Sbjct: 166 NYPSSTLVRGIAPALAAGCSAVVKPAETTPFTALMIADLLIRAGLPAGVVNVVTGTGIAA 225

Query: 269 GDTVTSSEHLCGINFTGSVPTFKHLWRQVAQNLDRFRTFPRLAGECGGKNFHFVHSSADV 328
           G  +     +  + FTGSV T   + + VA N+        L  E GGK+       A+V
Sbjct: 226 GAPLVRDPRVRHVTFTGSVATGVGVMQSVAPNVTG------LTLELGGKSPLVAFGDANV 279

Query: 329 DSVVSGTLRSAFEYGGQKCSACSRLYVPKSLWPQIKGRLLEEHSRIKVGDPAEDFGTFFS 388
           D+VV G L + F   GQ CSA SRL + +SL  +++ +L+    R++VG      G    
Sbjct: 280 DAVVEGALWAIFSNAGQICSAGSRLVIHRSLHAEVRDKLVARAQRLRVGHGLR--GPDIG 337

Query: 389 AVIDAKAFARIKKWLEHARSSPSLSILAGGQCNESV----GYYVEPCIIESKDPQEPIMK 444
           AV  A+  A+I   +  AR+   + I+ GG+    V    G++  P I++     +  + 
Sbjct: 338 AVNSARHLAQIDDHVSRARTR-GVEIVTGGEILTDVESGKGWFYAPTILDDLAANDDAVL 396

Query: 445 EEIFGPVLTVYVYPDDKYRETLQLVDSTTSYGLTGAVFAQDKAIVQEATRMLRNA-AGNF 503
           +EIFGPVL + V+ D+   E L L +  T + L   ++ +D   +  A RM R   AG  
Sbjct: 397 QEIFGPVLAIQVFEDE--AEALALANG-TEFALAAGIYTRD---IATALRMARRVDAGQV 450

Query: 504 YINDKSTGSVVGQQPFGGARASGTNDKPG 532
            +ND   G +  + PFGG R SG   + G
Sbjct: 451 TVNDYWAGGI--ELPFGGNRKSGFGREKG 477


Lambda     K      H
   0.319    0.135    0.411 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 586
Number of extensions: 29
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 562
Length of database: 494
Length adjustment: 35
Effective length of query: 527
Effective length of database: 459
Effective search space:   241893
Effective search space used:   241893
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory